JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / io / FastaFile.java

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 9aff348..ec1c82e 100755 (executable)
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,10 +20,13 @@
  */
 package jalview.io;
 
-import java.io.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 
-
-import jalview.datamodel.*;
+import java.io.IOException;
 
 /**
  * DOCUMENT ME!
@@ -74,12 +77,13 @@ public class FastaFile extends AlignFile
    * @throws IOException
    *           DOCUMENT ME!
    */
+  @Override
   public void parse() throws IOException
   {
     StringBuffer sb = new StringBuffer();
     boolean firstLine = true;
 
-    String line,uline;
+    String line, uline;
     Sequence seq = null;
 
     boolean annotation = false;
@@ -141,23 +145,24 @@ public class FastaFile extends AlignFile
       seqs.addElement(seq);
     }
   }
+
   private AlignmentAnnotation makeAnnotation(SequenceI seq, StringBuffer sb)
   {
     Annotation[] anots = new Annotation[sb.length()];
     char cb;
-    for (int i=0;i<anots.length;i++)
+    for (int i = 0; i < anots.length; i++)
     {
       char cn = sb.charAt(i);
       if (cn != ' ')
       {
-        anots[i] = new Annotation(""+cn, null,
-              ' ', Float.NaN);
+        anots[i] = new Annotation("" + cn, null, ' ', Float.NaN);
       }
     }
     AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName()
             .substring(2), seq.getDescription(), anots);
     return aa;
   }
+
   /**
    * called by AppletFormatAdapter to generate an annotated alignment, rather
    * than bare sequences.
@@ -169,8 +174,7 @@ public class FastaFile extends AlignFile
     addProperties(al);
     for (int i = 0; i < annotations.size(); i++)
     {
-      AlignmentAnnotation aa = (AlignmentAnnotation) annotations
-              .elementAt(i);
+      AlignmentAnnotation aa = annotations.elementAt(i);
       aa.setPadGaps(true, al.getGapCharacter());
       al.addAnnotation(aa);
     }
@@ -205,7 +209,8 @@ public class FastaFile extends AlignFile
 
       out.append(newline);
 
-      int nochunks = (s[i].getLength() / len) + 1;
+      int nochunks = (s[i].getLength() / len)
+              + (s[i].getLength() % len > 0 ? 1 : 0);
 
       for (int j = 0; j < nochunks; j++)
       {
@@ -234,6 +239,7 @@ public class FastaFile extends AlignFile
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public String print()
   {
     return print(getSeqsAsArray());